Revisiting the coding potential of the E. coli genome through Hfq co-immunoprecipitation.
Revisiting the coding potential of the E. coli genome through Hfq co-immunoprecipitation.
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DOI：
10.4161/rna.29299
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发表时间：
2014
期刊：
影响因子：
4.1
通讯作者：
Lybecker M
中科院分区：
文献类型：
--
作者：
Bilusic I;Popitsch N;Rescheneder P;Schroeder R;Lybecker M
Hfq是细菌适应环境条件变化时基因表达的全局调节因子。其主要功能是促进调节性小RNA（sRNA）与其靶mRNA之间的RNA-RNA相互作用。以前，我们证明了Hfq在体外结合许多反义RNA（asRNA），并假设Hfq可能通过asRNA在调节基因表达中发挥作用。为了研究E. coli Hfq结合转录组中更详细地，我们共免疫沉淀和深度测序RNA结合Hfq在体内。我们检测到许多新的Hfq结合sRNAs，并观察到近300种mRNA与Hfq结合。其中，几种已知是sRNA靶标。我们鉴定了25种新的RNA，它们是从蛋白质编码区内转录的，并将它们命名为基因内RNA（intraRNA）。此外，67个asRNA与Hfq共免疫沉淀，证明Hfq在体内结合反义转录物。北方印迹分析证实了深度测序结果，并证明许多新的Hfq结合RNA鉴定的Hfq的调节。
Hfq is a global regulator of gene expression in bacteria undergoing adaptation to changing environmental conditions. Its major function is to promote RNA-RNA interactions between regulatory small RNAs (sRNAs) and their target mRNAs. Previously, we demonstrated that Hfq binds many antisense RNAs (asRNAs) in vitro and hypothesized that Hfq may play a role in regulating gene expression via asRNAs. To investigate the E. coli Hfq-binding transcriptome in more detail, we co-immunoprecipitated and deep-sequenced RNAs bound to Hfq in vivo. We detected many new Hfq-binding sRNAs and observed that almost 300 mRNAs bind to Hfq. Among these, several are known to be sRNA targets. We identified 25 novel RNAs, which are transcribed from within protein coding regions and named them intragenic RNAs (intraRNAs). Furthermore, 67 asRNAs were co-immunoprecipitated with Hfq, demonstrating that Hfq binds antisense transcripts in vivo. Northern blot analyses confirmed the deep sequencing results and demonstrated that many of the novel Hfq-binding RNAs identified are regulated by Hfq.